Negative staining with zinc-imidazole of gel electrophoresis-separated nucleic acids

Production of bioactive recombinant ovine cysteine-rich secretory protein 1 in Escherichia coli

Ovine cysteine-rich secretory protein 1 (CRISP-1) is an acidic glycoprotein of epididymal origin under CRISP, antigen 5, pathogenesis-related protein 1 (CAP) super-family. The aim of the present study was the optimization of bacterial production and partial characterization of putative mature ovine CRISP-1 protein. The cDNA corresponding to T^{23 -} C²⁴² peptide fragment of ovine CRISP-1 protein was cloned into THE pET32b(+) expression vector using E. coli DH5α. Protein expression was carried out in E. coli BL21(DE3) by inducition with 1 mM IPTG at 37°C for 4 h. The recombinant protein was expressed as inclusion bodies and purified by Ni-NTA affinity chromatography using a pH gradient. Further purification of the protein was carried out by gel extraction following zinc sulfate negative staining. SDS-PAGE analysis of the purified recombinant CRISP-1 protein revealed a 43.8 kDa band. Bioactivity of the purified CRISP-1 protein was examined on sperm motility and capacitation. The recombinant ovine CRISP-1 protein at 5 µg/ml caused significant inhibition of sperm motility, and the activity was lost following heating the protein at 100°C for 5 min. The protein also demonstrated decapacitation activity, and at a concentration of 2 µg/ml, it caused a significant (P < 0.05) reduction in sperm capacitation. In conclusion, the thioredoxin-tagged ovine CRISP-1 protein was successfully produced in E. coli and purified in the soluble form by a combination of Ni-NTA affinity chromatography, gel purification, and dialysis. The recombinant protein exhibited both motility-inhibiting and decapacitating activities. Further study is needed to elucidate the mechanism of action and evaluate it's possible use in semen preservation.Abbreviations: CRISP-1: Cysteine-rich secretory protein-1; PCR: polymerase chain reaction; IPTG: isopropyl-β-D-thiogalactopyranoside; LB: Luria Bertani; SDS-PAGE: sodium dodecyl sulfate polyacrylamide gel electrophoresis; EDTA: ethylene diamine tetraacetic acid; Ni-NTA: Nickel nitrilotriacetic acid.

Revisit of Imidazole-Zinc Reverse Stain for Protein Polyacrylamide Gel Electrophoresis

Imidazole-zinc reverse stain (ZN stain) is known for high sensitivity, ease of use, and cost-effective feature. ZN stain is compatible to many experiments of which those are proteomics-related in particular. Here, we describe the ZN staining procedures and the subsequent procedures incorporated in detail, along with the improvements of setup in aspects of visualization and documentation for postprocessing ZN stained gel images.

A highly sensitive nucleic acid stain based on amino-modified tetraphenylethene: the influence of configuration

We designed and synthesized a new amino-functionalized tetraphenylethene (TPE) derivative as a highly sensitive dye for the detection of dsDNA and oligonucleotide in both solution and a gel matrix. We further revealed that the cis configuration dye showed a much higher sensitivity than its trans isomer for the first time.

A coordination complex system for generic, ultrafast, and sensitive multimode fluorescent staining of biomolecules

Gel electrophoresis staining methodologies documented thus far are largely utilized in a biomolecule context-dependent manner. We report herein the development of a generic, ultrafast, and sensitive multimode fluorescent system for the efficient identification of DNA, RNA, and proteins. Interaction between a positively charged, planar ligand-based coordination complex with partner biomolecule leads to aggregation-induced fluorescence quenching and allows for the image contrast generation within one minute. Alternatively, successive reactions of the biomolecule-loaded gel with cation and ligand, in either order of sequence, provide an equally effective staining efficacy. Image contrast reversal is accomplished through a facile washing or photobleaching procedure. The versatility in the applicable target species and signal generation modes provides a hint at the design of novel staining structures and potentially enables the high-throughput readout of biomolecules.

Revisit of imidazole-zinc reverse stain for protein polyacrylamide gel electrophoresis

Imidazole-zinc reverse stain (ZN stain) is known for its high sensitivity, ease of use, and cost-effective feature. ZN stain is compatible to many experiments of which those are proteomics-related in particular. Here, we describe the ZN staining procedures and the subsequent procedures incorporated in detail, along with the improvements of setup in aspects of visualization and documentation for post-processing ZN-stained gel images.

Quantitative proteomics: assessing the spectrum of in-gel protein detection methods

Proteomics research relies heavily on visualization methods for detection of proteins separated by polyacrylamide gel electrophoresis. Commonly used staining approaches involve colorimetric dyes such as Coomassie Brilliant Blue, fluorescent dyes including Sypro Ruby, newly developed reactive fluorophores, as well as a plethora of others. The most desired characteristic in selecting one stain over another is sensitivity, but this is far from the only important parameter. This review evaluates protein detection methods in terms of their quantitative attributes, including limit of detection (i.e., sensitivity), linear dynamic range, inter-protein variability, capacity for spot detection after 2D gel electrophoresis, and compatibility with subsequent mass spectrometric analyses. Unfortunately, many of these quantitative criteria are not routinely or consistently addressed by most of the studies published to date. We would urge more rigorous routine characterization of stains and detection methodologies as a critical approach to systematically improving these critically important tools for quantitative proteomics. In addition, substantial improvements in detection technology, particularly over the last decade or so, emphasize the need to consider renewed characterization of existing stains; the quantitative stains we need, or at least the chemistries required for their future development, may well already exist.

A comprehensive evaluation of imidazole-zinc reverse stain for current proteomic researches

In this paper, we comprehensively evaluated the capability of imidazole-zinc reverse stain (ZN) in comparative proteomics. Three commonly used protein gel staining methods, including silver (SN), SYPRO Ruby (SR), and CB stain were investigated alongside for comparison purpose. A transparency scanning procedure, which may deliver more even and contrasting gel images, was found best for documenting ZN stained gels. Our results showed that ZN was more sensitive than SN, SR, and CB. It may reveal as few as 1.8 ng of proteins in a gel. Moreover, ZN was found to provide a linear dynamic range of staining for revealing proteins up to 140 ng, and show an insignificant staining preference. To analyze a ZN stained 2-D gel image that generally comprises an apparent but even background, the Melanie 4 software was found more suitable than others. Furthermore, ZN demonstrated an equivalent or better MS compatibility than the other three staining methods. Intense and comprehensive MS profiles were frequently observed for ZN stained gel spots. Approximate two-third of ZN stained gel spots were successfully identified for protein identities. Taken together, our results suggest that the prompt, cost effective and versatile ZN is well suited for current proteomic researches.

Negative detection of biomolecules separated in polyacrylamide electrophoresis gels

Here we describe the protocols for negative or reverse detection of proteins, nucleic acids and lipopolysaccharides separated in polyacrylamide electrophoresis gels. These protocols are based on the selective synthesis and precipitation of a white imidazole-zinc complex in the gel, which is absent from those zones where biomolecules are located. These methods are highly sensitive (1-10 ng of biomolecules per band), very cheap as they use inexpensive, common laboratory reagents (imidazole and a Zn II salt), rapid (less than 20 min after gel washing), robust and simple (two steps). Reverse-stained biomolecules are reversibly fixed in the gel. After brief incubation in a zinc chelating agent, biomolecules can be recovered from the gel with the same efficiency as from unstained gels. In consequence, they are procedures of choice for micropreparative applications. References covering typical applications are included.

"Reverse-staining" of biomolecules in electrophoresis gels: analytical and micropreparative applications

Negative or reverse staining using imidazole and zinc salts for protein detection in electrophoresis gels was originally introduced in 1990. The method is based on the selective precipitation of zinc imidazolate in the gel except in the zones where proteins are located. The method was later adapted to allow high-sensitivity negative detection of nucleic acids and bacterial lipopolysaccharides. It provides a practically quantitative recovery of intact biomolecules and is a method of choice for micropreparative applications of gel electrophoresis to proteomics and similar structural studies. Zinc-mediated protein fixation in the gel is fully reversible and the eluted biomolecules are neither chemically modified nor contaminated with organic dyes. Here we present a detailed compilation of practical methods for implementing these techniques with emphasis in their analytical or micropreparative applications.

Detection of biomolecules in electrophoresis gels with salts of imidazole and zinc II: a decade of research

The proven ability of gel electrophoresis to simultaneously resolve, in a single experiment, many components from complex biological samples, has determined its preference over a variety of well-established chromatographic methods. Therefore, procedures placed at the interface between gel separation and microanalysis have earned increasing significance with respect to the overall success of the microanalytical strategy. The first of these procedures is the detection technique. The most important requirement for compatibility with further analysis or bioapplications is that the staining method does not compromise the chemical integrity and the biological properties of micropurified biomolecules. Procedures for negative detection of proteins with metal salts that have been proven to comply with this condition have been known for about 15 years. Only recently have these procedures been extended to the field of nucleic acids and lipopolysaccharides. The focus of this review is to chronicle the development and current status of the negative or reverse stain procedure based on the in-gel reaction of imidazole with zinc salts and its applications forthe micropurification and analysis of unmodified proteins, nucleic acids and bacterial lipopolysaccharides. We highlight the common aspects in the detection of the three types of biomolecules, and their applications to structural and biological analyses. Emphasis is given on the mechanism underlying imidazole-zinc staining, as it contributes to a deeper understanding of a general detection mechanism with metal salts. Finally, we discuss the latest applications of the techniques in proteomics and their possible impact on the characterization of gel-separated single components from complex lipopolysaccharides.

Efficient purification of DNA fragments using a protein binding membrane

A novel and efficient method has been developed for isolation of correctly digested DNA fragments without the use of classic size-dependent electrophoretic separation methods. To achieve this, DNA fragments are end-labelled by haptens. After specific endonuclease digestion of the hapten-labelled DNA, the DNA is incubated with a protein that specifically binds to the hapten. The incubation mixture is then passed through a cartridge containing a protein-binding membrane that does not bind DNA. Undigested and partly digested DNA are retained on the membrane, while correctly digested DNA is selectively recovered for use in further downstream applications.

Understanding the mechanism of the zinc-ion stains of biomacromolecules in electrophoresis gels: generalization of the reverse-staining technique

We have recently shown that a few nanograms of protein separated by electrophoresis in sodium dodecyl sulfate-polyacrylamide gels can be detected by reverse-staining, exploiting the precipitation reaction between zinc(II) and imidazole. Modifications of this method have also been generated to detect gel-isolated nucleic acids and bacterial glycolipids. Because there is no recourse to chemical modifiers, the reverse-staining technique has been valuable when micropreparing these biomacromolecules for later use or characterization. The mechanism underlying the reverse-staining effect, however, remains incompletely understood and this has prevented a further generalization of the technique. Here, we have conducted physicochemical experiments and identified zinc imidazolate (ZnIm2) as the main component of the precipitate that forms along the surface of zinc-imidazole reverse-stained gels. Many staining effects observed when gels containing electrophoretically separated biopolymers are subjected to zinc-imidazole stains have been rationalized. The reverse-staining method has been vastly generalized, now allowing the detection of proteins and glycolipids as well as complexes of these macromolecules in native gels. We demonstrate the application of the reverse-staining technique in situations where Coomassie blue or silver staining was inappropriate or failed to produce detection of the species of interest. The present generalization of the reverse-staining method facilitated the characterization of biomacromolecular interaction partners in mixtures of bacterial glycolipids and human tears.

Elution of lipopolysaccharides from polyacrylamide gels

A simple procedure for elution in water of bacterial lipopolysaccharides (LPS) from sodium dodecyl sulfate-polyacrylamide gels is described. It consists of the combination of three principal steps: first, highly sensitive on-gel LPS detection (1-10 ng/band) with zinc-imidazole (negative or reverse staining); second, washing of the individual LPS band in a solution of a zinc-complexing agent (e.g., 100 mM EDTA); and finally, elution of the LPS (100-200 microliters water for a 0.5-microgram LPS band) from gel microparticles for 3 h at room temperature. Using this procedure, we have successfully eluted a variety of LPS forms from Bordetella pertussis, Escherichia coli 0111:B4, E. coli K-235, Salmonella enteritidis, and Pseudomonas aeruginosa. Elution recovery of rough or semismooth LPS was about 70-80%, while that of smooth LPS was only about 10%. Eluted LPS was biologically active as tested by limulus amebocyte lysate and TNF-alpha assays.

A procedure for protein elution from reverse-stained polyarcylamide gels applicable at the low picomole level: An alternative route to the preparation of low abundance proteins for microanalysis

We developed a technique that allows rapid protein elution from polyacrylamide gel bands at room temperature into a detergent-free buffer (elution time 2 x 10 min, total working time about 30 min) with high yields (90-98%) even at a low picomole level (1 picomole per band). Its efficacy relies on the combination of protein detection by reverse staining with the enhancement of protein diffusion after gel crushing. Detection is accomplished by gel incubation in an imidazole solution, followed by incubation in a zinc salt solution to develop a negative stain pattern. Proteins are eluted by zinc complexation in Laemmli electrophoresis buffer (Tris + glycine), from which sodium dodecyl sulfate is omitted to allow direct subsequent microanalysis, e.g. high performance liquid chromatography (HPLC) and automatic sequencing. A variety of proteins were eluted efficiently (with no apparent restriction due to their intrinsic properties) as quantified with radioiodinated total E. coli proteins. Yields were independent of acrylamide concentration, protein molecular mass (from 10 to 100 kDa) and the amount (from 1 to 100 picomole) of protein in the band. This protocol was derived from a quantitative evaluation of the effect of protein staining and of sample reduction prior to electrophoresis on elution yields. For N-terminal sequencing, the protein eluate was automatically loaded on a polyvinylidene difluoride (PVDF) membrane with conventional HPLC equipment; both loading and membrane clean-up were monitored at 206 nm. By simultaneously processing several analytical bands, the procedure allowed trace enrichment of a natural scarce protein that was N-terminal sequenced.